Dear Karunakaran, I don't think there is any error here. I have also made MD simulations of HIV-PR dimer with Gromacs, but I couldn't observed complete seperation of dimer to monomers. It seems after 1ns simulation, there is a seperation between tips of flaps. (I mean the seperation between Gly49, Ile50, Gly51 and Gly49', Ile50', Gly51').I measured about 5 Angstrom seperation (average), distance between the alpha carbon atoms for these residues after simulation. When you put some inhibitors to this cavity, this seperation may restricted. You may check the article: Schuster et al, Biochemistry, 42, 1326, 2003. Serdar Durdagi
chandran karunakaran <[EMAIL PROTECTED]> schrieb: Dear GMX users, On running the MD for HIV protease as dimer structure, it gets separated after the energy minimization. (Thats dimer is separated into two monomers). Could you kindly help me out in running HIV protease as dimer? with thanks c.karunakaran *******************************+ Dr.Karunakaran Chandran + Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226 + Resi.: 414-443-0085 + Off : 414-456-4034 + ******************************** ____________________________________________________________________________________ Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. http://farechase.yahoo.com/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Heute schon einen Blick in die Zukunft von E-Mails wagen? Versuchen Sie´s mit dem neuen Yahoo! Mail.
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